Table 1.

Preprocessing of DNA methylation microarray data

Normalization	Bias	Statistical Method	Reference
Within-array	Dye-bias for two-color microarrays Dye-bias + sequence bias + restriction cut-site density	Loess normalization, using a subset of CpG- free regions Linear model	Ordway et al. (2006); Irizarry et al. (2008) Potter et al. (2008)
	Background fluorescence	Normal-exponential convolution, using CpG-free regions to estimate the background distribution and stratifying on GC content	Aryee et al. (2010)
	Fragment length	Quantile normalization by fragment length	Thompson et al. (2008)
Between-Array	Array-specific effects	Subset quantile normalization	Aryee et al. (2010)